[med-svn] r13414 - trunk/packages/flexbar/trunk/debian
Tony Travis
ajtravis-guest at alioth.debian.org
Thu Apr 25 09:33:47 UTC 2013
Author: ajtravis-guest
Date: 2013-04-25 09:33:47 +0000 (Thu, 25 Apr 2013)
New Revision: 13414
Modified:
trunk/packages/flexbar/trunk/debian/changelog
trunk/packages/flexbar/trunk/debian/copyright
trunk/packages/flexbar/trunk/debian/flexbar.1
Log:
Updated for Flexbar v2.33
Modified: trunk/packages/flexbar/trunk/debian/changelog
===================================================================
--- trunk/packages/flexbar/trunk/debian/changelog 2013-04-25 09:29:53 UTC (rev 13413)
+++ trunk/packages/flexbar/trunk/debian/changelog 2013-04-25 09:33:47 UTC (rev 13414)
@@ -1,5 +1,7 @@
-flexbar (2.32-1) unstable; urgency=low
+flexbar (2.33-1) unstable; urgency=low
+ * Updated from new upstream sources
+
* Initial release (Closes: #701539)
- -- Tony Travis <ajt at minke.ukfsn.org> Sat, 23 Feb 2013 11:24:05 +0000
+ -- Tony Travis <ajt at minke.ukfsn.org> Mon, 22 Apr 2013 16:58:06 +0000
Modified: trunk/packages/flexbar/trunk/debian/copyright
===================================================================
--- trunk/packages/flexbar/trunk/debian/copyright 2013-04-25 09:29:53 UTC (rev 13413)
+++ trunk/packages/flexbar/trunk/debian/copyright 2013-04-25 09:33:47 UTC (rev 13414)
@@ -29,18 +29,6 @@
On Debian systems, the complete text of the GNU General
Public License version 3 can be found in "/usr/share/common-licenses/GPL-3".
-Files: include/tbb/*
-Copyright: Copyright (c) 2005-2011 Intel Corporation
-License: GPLv2_runtime_exception
- This program makes use of the TBB (Threading Building Blocks) library.
- see <http://threadingbuildingblocks.org/>. Specifically, the TBB open-source
- license is the same license used by the GNU libstdc++ library in gcc 4.2.1
- (and earlier).
- .
- For a complete description of the TBB license, please visit the official GNU
- website for GPLv2 and the runtime exception.
- <http://www.gnu.org/licenses/old-licenses/gpl-2.0.html>
-
Files: include/seqan/*
Copyright: © 2007-2010
Andreas Döring <doering at inf.fu-berlin.de>
Modified: trunk/packages/flexbar/trunk/debian/flexbar.1
===================================================================
--- trunk/packages/flexbar/trunk/debian/flexbar.1 2013-04-25 09:29:53 UTC (rev 13413)
+++ trunk/packages/flexbar/trunk/debian/flexbar.1 2013-04-25 09:33:47 UTC (rev 13414)
@@ -1,47 +1,51 @@
-.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.40.10.
-.TH FLEXBAR "1" "February 2013" "flexbar version 2.32" "User Commands"
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.40.4.
+.TH FLEXBAR "1" "April 2013" "flexbar " "User Commands"
.SH NAME
-flexbar \- flexible barcode and adapter removal for sequencing platforms
-.SH SYNOPSIS
+flexbar \- manual page for flexbar
+.SH DESCRIPTION
+flexbar \- flexible barcode and adapter removal
+.PP
+SYNOPSIS
.IP
flexbar \fB\-t\fR target \fB\-f\fR format \fB\-r\fR
reads [\-b barcodes] [\-a adapters]
[options]
.PP
-.SH OPTIONS
+DESCRIPTION
.HP
\fB\-h\fR, \fB\-\-help\fR
.IP
-Display this help message
+Displays this help message.
.HP
-\fB\-v\fR, \fB\-\-version\fR
+\fB\-\-version\fR
.IP
-Display program version
+Display version information
.HP
\fB\-c\fR, \fB\-\-cite\fR
.IP
-View citation information
+Shows citation information.
.IP
Basic options:
.HP
\fB\-n\fR, \fB\-\-threads\fR NUM
.IP
-Number of threads, default:
-1
+Number of threads. Default:
+1.
.HP
\fB\-t\fR, \fB\-\-target\fR STR
.IP
-Prefix for output file names
+Prefix for output file
+names.
.HP
\fB\-r\fR, \fB\-\-reads\fR FILE
.IP
Input file with reads, that
-may contain barcodes
+may contain barcodes.
.HP
\fB\-p\fR, \fB\-\-reads2\fR FILE
.IP
Second input file for paired
-read scenario
+read scenario.
.HP
\fB\-f\fR, \fB\-\-format\fR STR
.IP
@@ -50,7 +54,7 @@
fastq, fastq\-sanger,
fastq\-solexa, fastq\-i1.3,
fastq\-i1.5, fastq\-i1.8
-(illumina 1.8+)
+(illumina 1.8+).
.IP
Barcode detection:
.HP
@@ -58,60 +62,57 @@
.IP
Fasta file with barcodes,
specify (br) to use separate
-barcode reads
+barcode reads.
.HP
\fB\-br\fR, \fB\-\-barcode\-reads\fR FILE
.IP
Fasta or fastq file with
separate barcode reads, if
-not within reads
+not within reads.
.HP
\fB\-be\fR, \fB\-\-barcode\-trim\-end\fR STR
.IP
Type of barcoding within
reads, see section trim\-end
-modes, default: ANY
+modes. Default: ANY.
.HP
\fB\-bn\fR, \fB\-\-barcode\-tail\-length\fR NUM
.IP
Number of bases for tail
-trim\-end types, default:
-barcode length
+trim\-end modes. Default:
+barcode length.
.HP
\fB\-bo\fR, \fB\-\-barcode\-min\-overlap\fR NUM
.IP
Minimum overlap of barcode
-and read, default: barcode
-length
+and read. Default: barcode
+length.
.HP
\fB\-bt\fR, \fB\-\-barcode\-threshold\fR NUM
.IP
Allowed mismatches and
indels per 10 bases for
-barcode, default: 1.0
+barcode. Default: 1.0.
.HP
\fB\-bk\fR, \fB\-\-barcode\-keep\fR
.IP
Keep barcodes within reads
-instead of removal
+instead of removal.
.HP
-\fB\-ba\fR, \fB\-\-barcode\-tag\-length\fR NUM
-.IP
-Use random code with given
-size upstream barcode for
-read tagging
-.HP
\fB\-bm\fR, \fB\-\-barcode\-match\fR NUM
.IP
-Match score, default: 1
+Alignment match score.
+Default: 1.
.HP
\fB\-bi\fR, \fB\-\-barcode\-mismatch\fR NUM
.IP
-Mismatch score, default: \fB\-1\fR
+Alignment mismatch score.
+Default: \fB\-1\fR.
.HP
\fB\-bg\fR, \fB\-\-barcode\-gap\fR NUM
.IP
-Gap score, default: \fB\-7\fR
+Alignment gap score.
+Default: \fB\-7\fR.
.IP
Adapter removal:
.HP
@@ -119,123 +120,130 @@
.IP
Fasta file with adapters, or
barcodes to remove within
-reads
+reads.
.HP
\fB\-as\fR, \fB\-\-adapter\-seq\fR STR
.IP
Single adapter sequence as
alternative to adapters
-option
+option.
.HP
\fB\-ae\fR, \fB\-\-adapter\-trim\-end\fR STR
.IP
-Type of alignment for
-removal, see section
-trim\-end modes, default:
-RIGHT
+Type of adapter removal, see
+section trim\-end modes.
+Default: RIGHT.
.HP
\fB\-an\fR, \fB\-\-adapter\-tail\-length\fR NUM
.IP
Number of bases for tail
-trim\-end types, default:
-adapter length
+trim\-end modes. Default:
+adapter length.
.HP
\fB\-ao\fR, \fB\-\-adapter\-min\-overlap\fR NUM
.IP
Minimum overlap of adapter
-and read, default: 1
+and read. Default: 1.
.HP
\fB\-at\fR, \fB\-\-adapter\-threshold\fR NUM
.IP
Allowed mismatches and
indels per 10 bases for
-adapter, default: 3.0
+adapter. Default: 3.0.
.HP
\fB\-am\fR, \fB\-\-adapter\-match\fR NUM
.IP
-Match score, default: 1
+Alignment match score.
+Default: 1.
.HP
\fB\-ai\fR, \fB\-\-adapter\-mismatch\fR NUM
.IP
-Mismatch score, default: \fB\-1\fR
+Alignment mismatch score.
+Default: \fB\-1\fR.
.HP
\fB\-ag\fR, \fB\-\-adapter\-gap\fR NUM
.IP
-Gap score, default: \fB\-7\fR
+Alignment gap score.
+Default: \fB\-7\fR.
.IP
Filtering and trimming:
.HP
\fB\-u\fR, \fB\-\-max\-uncalled\fR NUM
.IP
Allowed uncalled bases (N or
-\&.) in reads, default: 0
+\&.) in reads. Default: 0.
.HP
\fB\-x\fR, \fB\-\-pre\-trim\-left\fR NUM
.IP
Trim specified number of
bases on 5' end of reads
-before detection
+before detection.
.HP
\fB\-y\fR, \fB\-\-pre\-trim\-right\fR NUM
.IP
Trim specified number of
bases on 3' end of reads
-before detection
+before detection.
.HP
\fB\-q\fR, \fB\-\-pre\-trim\-phred\fR NUM
.IP
Trim 3' end until specified
-or higher quality reached,
-precise fastq format
+or higher quality reached.
.HP
\fB\-z\fR, \fB\-\-post\-trim\-length\fR NUM
.IP
Trim to specified read
length from 3' end after
-removal
+removal.
.HP
\fB\-m\fR, \fB\-\-min\-readlength\fR NUM
.IP
Minimum read length to
-remain after removal,
-default: 18
+remain after removal.
+Default: 18.
.IP
Logging and tagging:
.HP
\fB\-l\fR, \fB\-\-log\-level\fR STR
.IP
-Print alignments for all or
-modified reads. One of ALL,
-MOD, and TAB
+Print valid sequence
+alignments of reads. One of
+ALL, MOD, and TAB.
.HP
\fB\-s\fR, \fB\-\-single\-reads\fR
.IP
-Output single reads of
-patially too short paired
-reads
+Output single reads for
+partially too short paired
+reads.
.HP
-\fB\-d\fR, \fB\-\-length\-dist\fR
-.IP
-Write length distribution
-for read output files
-.HP
\fB\-o\fR, \fB\-\-fasta\-output\fR
.IP
Prefer non\-quality formats
-fasta and csfasta for output
+fasta and csfasta for
+output.
.HP
+\fB\-i\fR, \fB\-\-length\-dist\fR
+.IP
+Write length distribution
+for read output files.
+.HP
\fB\-e\fR, \fB\-\-number\-tags\fR
.IP
Replace read tags by
ascending number to save
-space
+space.
.HP
\fB\-g\fR, \fB\-\-removal\-tags\fR
.IP
Tag reads that are subject
to adapter or barcode
-removal
+removal.
+.HP
+\fB\-d\fR, \fB\-\-random\-tags\fR
.IP
+Random read tags at barcode
+or adapter positions with N.
+.IP
Trim\-end modes:
.IP
ANY: longer part of read remains
@@ -248,14 +256,32 @@
RIGHT_TAIL: use only last n bases,
see tail\-length options
.PP
-.SH EXAMPLES
+EXAMPLES
.IP
flexbar \fB\-t\fR target \fB\-f\fR fastq\-i1.3 \fB\-r\fR
reads.fastq \fB\-b\fR bar.fasta \fB\-a\fR
adap.fasta
-.IP
flexbar \fB\-t\fR target \fB\-f\fR csfastq \fB\-r\fR
reads.csfastq \fB\-a\fR adapters.fasta
\fB\-ae\fR LEFT
.PP
+VERSION
+.IP
+flexbar version: 2.33
+Last update March 18, 2013
+.PP
Further documentation on: flexbar.sourceforge.net
+.PP
+flexbar version 2.33
+.SH "SEE ALSO"
+The full documentation for
+.B flexbar
+is maintained as a Texinfo manual. If the
+.B info
+and
+.B flexbar
+programs are properly installed at your site, the command
+.IP
+.B info flexbar
+.PP
+should give you access to the complete manual.
More information about the debian-med-commit
mailing list